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- PDB-3rfa: X-ray structure of RlmN from Escherichia coli in complex with S-a... -

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Basic information

Entry
Database: PDB / ID: 3rfa
TitleX-ray structure of RlmN from Escherichia coli in complex with S-adenosylmethionine
ComponentsRibosomal RNA large subunit methyltransferase N
KeywordsOXIDOREDUCTASE / radical sam / S-adenosylmethionine / iron sulfur cluster / methyltransferase
Function / homology
Function and homology information


23S rRNA (adenine2503-C2)-methyltransferase / tRNA (adenine(37)-C2)-methyltransferase activity / rRNA (adenine(2503)-C2-)-methyltransferase activity / tRNA methylation / rRNA base methylation / 4 iron, 4 sulfur cluster binding / tRNA binding / rRNA binding / response to antibiotic / metal ion binding / cytosol
Similarity search - Function
Ribosomal RNA large subunit methyltransferase RlmN/Cfr / Dual-specificity RNA methyltransferase RlmN / Methyltransferase (Class A) / : / Ribosomal RNA large subunit methyltransferase N-terminal domain / DNA polymerase; domain 1 - #530 / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / DNA polymerase; domain 1 ...Ribosomal RNA large subunit methyltransferase RlmN/Cfr / Dual-specificity RNA methyltransferase RlmN / Methyltransferase (Class A) / : / Ribosomal RNA large subunit methyltransferase N-terminal domain / DNA polymerase; domain 1 - #530 / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / DNA polymerase; domain 1 / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / Dual-specificity RNA methyltransferase RlmN
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBoal, A.K. / Grove, T.L. / McLaughlin, M.I. / Yennawar, N. / Booker, S.J. / Rosenzweig, A.C.
CitationJournal: Science / Year: 2011
Title: Structural basis for methyl transfer by a radical SAM enzyme.
Authors: Boal, A.K. / Grove, T.L. / McLaughlin, M.I. / Yennawar, N.H. / Booker, S.J. / Rosenzweig, A.C.
History
DepositionApr 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal RNA large subunit methyltransferase N
B: Ribosomal RNA large subunit methyltransferase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1586
Polymers90,6582
Non-polymers1,5004
Water3,261181
1
B: Ribosomal RNA large subunit methyltransferase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0793
Polymers45,3291
Non-polymers7502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Ribosomal RNA large subunit methyltransferase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0793
Polymers45,3291
Non-polymers7502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.180, 55.621, 252.179
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribosomal RNA large subunit methyltransferase N / 23S rRNA m2A2503 methyltransferase


Mass: 45328.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rlmN, yfgB, b2517, JW2501 / Production host: Escherichia coli (E. coli)
References: UniProt: P36979, 23S rRNA (adenine2503-C2)-methyltransferase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 10% PEG 6000, 5% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→126.09 Å / Num. all: 48139 / Num. obs: 47879 / % possible obs: 96.3 % / Observed criterion σ(F): 88.9 / Observed criterion σ(I): 5.4
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.05-2.09193.8
2.09-2.12195.2
2.12-2.16193.4
2.16-2.21195
2.21-2.26193.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.071 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 2421 5.1 %RANDOM
Rwork0.2016 ---
obs0.2037 43153 95.85 %-
all-48139 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.39 Å2 / Biso mean: 29.8012 Å2 / Biso min: 12.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20 Å2
2---0.76 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5463 0 70 181 5714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225637
X-RAY DIFFRACTIONr_angle_refined_deg1.0691.987634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5555690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46823.969262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35151016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7171550
X-RAY DIFFRACTIONr_chiral_restr0.0760.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214204
X-RAY DIFFRACTIONr_mcbond_it0.4131.53452
X-RAY DIFFRACTIONr_mcangle_it0.825586
X-RAY DIFFRACTIONr_scbond_it1.19432185
X-RAY DIFFRACTIONr_scangle_it2.084.52024
LS refinement shellResolution: 2.05→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 172 -
Rwork0.236 3196 -
all-3368 -
obs--93.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.72640.36380.31940.80990.39540.36960.02930.0182-0.04180.0996-0.0324-0.023-0.0045-0.04770.00310.0422-0.0071-0.02780.05410.01190.0333-9.18770.3049-48.1546
20.86240.62340.48340.78950.3580.5457-0.03060.0376-0.0006-0.1050.03430.009-0.04350.0293-0.00370.0776-0.00530.00980.0195-0.01710.0192-27.8344-5.1226-13.2105
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B17 - 375
2X-RAY DIFFRACTION2A17 - 349

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